The conformations of polypeptide chains where the main-chain parts of successive residues are enantiomeric. Their occurrence in cation and anion-binding regions of proteins

doi:10.1006/jmbi.2001.5228

Journal of Molecular Biology

Volume 315, Issue 2, 11 January 2002, Pages 183-191

https://doi.org/10.1006/jmbi.2001.5228 Get rights and content

Abstract

We have investigated the shapes of polypeptides where successive residues have main-chain φ,ψ conformations of opposite hand. A graph not unlike a Ramachandran plot is presented illustrating the various possible conformations. All are ring-shaped or extended. Some of these conformations occur in native proteins, the commonest approximating to a feature we propose calling a nest, described in the accompanying paper, where the main-chain NH groups point inwards relative to the ring and give rise to an anion-binding site. Another conformation is related but more extended and is found uniquely in the four stretches of polypeptide that line the tetrameric K⁺ channel; their CO groups bind the K ions in the channel. In a different ring-shaped conformation that we propose calling a catgrip, the main-chain CO groups point into the ring; this is employed for specific Ca ion binding in the annexin, phospholipase A2 and subtilisin loops, and the regularly arranged β-roll loops of the serralysin protease family.

Introduction

In the accompanying paper1 a novel feature is described that we call a nest to portray the depression formed by the NH groups of three consecutive residues that hydrogen bond to a negative, or partially negative, atom. Nests are found in a wide variety of different situations, some of functional importance. A depression of this sort is generated where the φ,ψ angles are about −90°,0° and 90°,0° (The average values for the commonest type of nest in native proteins are −90°,1°; 77°,21° but the principles remain relevant) such that successive residues are enantiomers of each other with regard to their main-chain structure. Nests frequently overlap, forming wider anion-binding depressions called compound nests.1 Such stretches of polypeptide have three or more adjacent residues with alternating enantiomeric conformations. This has led us to enquire whether other stretches of two or more enantiomeric residues may occur non-randomly in proteins and polypeptides.

To investigate more fully the range of possible structures with successive residues that are main-chain enantiomers we have constructed polyglycine computer models. The structures of polypeptides made from residues with identical conformations have been well studied,2 since they correspond to α-helices, β-strands and polyproline II helices. All these structures are helices of some sort. By contrast, those with alternating enantiomeric residues, which have not been considered before, are ring-shaped. Having examined their geometric properties, the rest of this article is aimed at finding structures in native proteins exhibiting these alternating enantiomeric conformations.

In the orifice of the potassium channel whose structure is known3 (current evidence suggests that many, if not all, potassium channels share this feature), the ion binds to the almost linearly arranged main-chain CO groups from the polypeptides of four subunits. This conformation qualifies as a compound nest according to the definition, but the component nests are more extended than typical nests, giving rise to the CO group arrangement. It also possesses approximately alternating enantiomeric main-chain residues.

We have also identified a loop that binds calcium ions via its main-chain carbonyl groups with a different alternating enantiomer main-chain structure. In one sense, this feature is already known, as it occurs in several calcium-binding proteins, but what is novel is the idea of regarding it as consisting of residues with enantiomeric main-chain conformations. This, in turn, points to possible relationships between the feature in various proteins. Such an easily defined feature deserves a name. We originally thought of calgrip (calcium grip) but propose catgrip (cation grip) in case any similar motifs are found at a future date that bind cations or positively charged groups other than calcium.

Catgrips consist of at least two successive residues with β_R and β_L conformations. This has the consequence that alternate CO groups are well positioned to grip a cation. As in nests, there are two enantiomeric forms of the catgrip, which are again called RL and LR. Also, catgrips can overlap to form RLR, LRL, RLRL, etc., features called compound catgrips; these are observed in some calcium-binding sites.

This search for structures with alternating enantiomeric residues has led to a consideration of anion and cation binding in proteins. Much is known about this topic.4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 Binding may be to side-chain or to main-chain groups, but we are concerned with the latter. Though without net charge, main-chain atoms are polar, such that NH groups often bind anions and CO groups bind cations. Frequently, NH groups from successive residues chelate anions, as has already been seen,1 while CO groups from residues close in sequence may bind cations. It turns out that that many of the alternating enantiomeric ring-shaped conformations we are describing are well suited to this purpose.

Section snippets

Polyglycine models

We built computer models of polyglycine polypeptides with a complete range of the possible alternating enantiomeric φ,ψ angles. Figure 1(a)-(h) are graphs showing various geometric features. They are like Ramachandran plots, except that in the original work2 only model polypeptide structures with identical conformations for successive residues were analysed. In Figure 1, if φ,ψ of one residue is −60°,10°, that for the alternating one is 60°,-10°. Because of this symmetric relationship, only

Conclusion

By making polyglycine computer models we have described the range of possible structures of polypeptides with alternating enantiomeric main-chain conformations for successive residues. The structures range from ring-shaped to extended. They are used to make Ramachandran-like plots, which allow various aspects of their shape to be explored. We have shown that polypeptides with such conformations occur regularly in certain situations in proteins. Three have been discovered. The commonest is the

Methods

The models in Figure 2 and the Ramachandran plots in Figure 1 derived from them were created by building the appropriate polyglycine polypeptides on computer using QUANTA software. 703 polypeptides differing by intervals of 10° for both φ and ψ were made. The rest of this article describes polypeptides in native proteins and synthetic cyclic peptides found to exhibit structures like those in Figure 1, Figure 2. To find them the Protein Data Bank and the Cambridge Crystallographic Database were

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^☆: Abbreviations used: enantiomerism refers to conformations related by what is commonly called mirror symmetry. RL and LR catgrips are defined as polypeptides where alternate main-chain CO groups bind a cation and where alternate residues have positive and negative φ values. In the RL sort, the first is negative; in the LR sort, the first is positive. β_R describes the main-chain conformation of an individual residue in the β conformation as seen in β-sheet. The R subscript distinguishes it from the enantiomeric β_L conformation. The NNN, OOO and OCCO angles are defined in the legend to Figure 1

¹: Edited by J. Thornton

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Journal of Molecular Biology

Regular articleThe conformations of polypeptide chains where the main-chain parts of successive residues are enantiomeric. Their occurrence in cation and anion-binding regions of proteins 1 ☆,

Abstract

Introduction

Section snippets

Polyglycine models

Conclusion

Methods

Advan. Protein Chem.

J. Mol Biol.

J. Mol. Biol.

Advan. Inorg. Chem.

Prog. Biophys. Mol. Biol.

Curr. Opin. Struct. Biol.

FEBS Letters

J. Mol. Biol.

J. Mol. Biol.

J. Mol. Biol.

Trends Biochem. Sci.

A novel main-chain anion binding site in proteinsthe nest. a particular combination of φ, ψ values in successive residues gives rise to anion binding sites that occur commonly and are often found at functionally important regions

J. Mol. Biol.

The structure of the potassium channelmolecular basis of K+ conduction and selectivity

Science

Structural aspects of metal ion - carboxylate interactions

J. Am. Chem. Soc.

Systematics in the interaction of metal ions with the main-chain carbonyl group in protein structure

Biochemistry

Interactions of metal ions with carboxylic and carboxamide groups in protein structures

Protein Eng.

Metalloenzymesstructural motifs and inorganic models

Science

Regular article
The conformations of polypeptide chains where the main-chain parts of successive residues are enantiomeric. Their occurrence in cation and anion-binding regions of proteins ¹ ☆,

The structure of the potassium channelmolecular basis of K⁺ conduction and selectivity